The PFA team included Chelsea's Gary Cahill at centre-back, alongside John Terry, and Ryan Bertrand at left-back, but Savage disagreed with those choices.
Savage felt that Cahill should have been replaced by Fonte and suggested that Bertrand hadn't had as good a season as Cresswell.
"I'd put Fonte in there ahead of Cahill and Cresswell should be in there, for me," the former Welsh international said. "I think Cresswell has been great."
Fonte has been a revelation in Southampton's defence and it was slightly surprising that he wasn't included.
Although Cahill has played a big part in Chelsea's success this term, he has not been an ever-present and Southampton actually have a better defensive record than the Blues, so Fonte can feel hard done by.
Cresswell, meanwhile, has been excellent for West Ham during his first season at Premier League level.
The summer signing has looked a threat going forward and has always been reliable at the back, meaning that his exclusion does appear harsh.